28 April 2008

Well, how about this BBC story headlined 'Darwin's footsteps: diving deep off South America's tip for climate change clues.' You click through and get this story about climate change in South America, which contains this:

"Charles Darwin came here in the 1830s.

It is where he began to formulate his Theory of Evolution, before sailing on to the Galapagos Islands."

I love the BBC, but from what I have read of Darwin's writings now available as primary sources at Darwin Online and the excellent biographies by Adrian Desmond and James Moore, and Janet Browne, this is a clanger. It was only in Darwin's ornithological notes on the Galapagos hummingbirds set down in late 1835 long after Beagle had left Tierra del Fuego that he writes that the 'stability of species' could be undermined should his specmens from different islands prove to be distinct varieties. His Beagle diaries for both visits to Tierra del Fuego betray no hint of what later became 'the species question'. He first committed his natural selection thoughts to paper in 1842, six years after he came ashore. (I am happy to be correct by more eminent Darwin scholars than I here...)

So, why the worry? Well, the British Broadcasting Corporation with educated correspondents, researchers and science reporters should not be getting the basics about a British hero of science so badly wrong. I emerged from my biology A level (precursor to my zoology B.Sc.) from a Yorkshire state school with only the vaguest knowledge of Charles Darwin and his work, and with absolutely no idea that he had posted his first copies of the Origin of Species from Ilkley only 50 miles from where I was being bored silly in double biology.

Other members of the Beagle Project management team have other hopes for what the rebuilt HMS Beagle will do. David Lort-Phillips (whose relative John Lort Stokes shared a cabin with Darwin and went on to become Beagle's captain on her third voyage to Australia) hopes that her voyage to Australia will move from the shadow of The Voyage with Darwin, and rightly so. Nunatak wants seas sampled, genomes shotgun sequenced, DNAs barcoded and greater science literacy among the general population.

I want every schoolchild in the country (and abroad) to be able to click a mouse and find out about Darwin (and Captain FitzRoy, who saw darwin safe around the world) through following a replica HMS Beagle as she sails and carries out her science and teaching work. Not everyone will become scientists, but they should carry on in their lives with Nunatak's improved scientific literacy and basic knowledge of how this giant of science came to establish one of the fundamental theories of biology. No science student should leave school without knowing this stuff, no BBC correspondent should sail Tierra del Fuego and write on their science pages in error about it. So, potential donor, that's why a replica HMS Beagle should be built.

26 April 2008

This has been a great week for HMS Beagle enthusiasts (such as your very own Beagle bloggers): we've been treated to five 15-minute episodes on BBC Radio 4 about the quest, led by Dr. Robert Prescott of the University of St. Andrews, to find her remains (most likely buried under five metres of mud in the river Roach in Essex).

And why it should matter to us whether we find the original Beagle's timbers? I liked Robert Prescott's answer, and I think it works just as well as a reason to build a new Beagle:

"It's a question of inspiration."

If you'd like to share in the inspiration, you can listen again to all five episodes here:

Episode 1A broad brush overview of the history of the ship from her birthplace at Woolwich dockyard in London, and moving reflections by Robert Prescott, Keith Thompson and Gordon Chancellor on the irony of her anonymous end in light of her now-famous contributions to science. Listen again and read my mini-review.

Episode 2Northward to Cambridge with Robert Prescott to learn more about Darwin's own thoughts about the little ship that was his home for five years.Listen again.

Episode 3Back to London, to the National Archives at Kew, and then down to Paglesham in Essex where the Beagle quietly lived out her tenure as a Coast Guard watch vessel; treasures emerge from the mudflats, but the mystery is still not solved. Listen again.

Episode 5 (Guest starring Beagle Project founders Peter McGrath and David Lort-Phillips!)Up to St. Andrews to analyse the cores extracted from the Beagle's likely final resting place - looking for diatoms and other denizens of the ship's sediments that might indicate passage through antipodean waters. Listen again.

Were Charles Darwin alive today, he would be a keen blogger. I mean, we've all seen how well suited his Beagle diaries are to the blog format, and, as anyone who's browsed Darwin-Online can tell you, to say the man was prolific would be a serious understatement.

And so it was with great delight that I discovered that Charles Darwin has indeed started a blog over on Nature Network called (wait for it...) Charles Darwin's blog. But don't let the rather mirthless name fool you; it's chock full of humour, history and, of course, science.

25 April 2008

Update:Welcome Pharyngula readers! After you look at the animation below, please stick around, explore the blog and learn more about our project to build a sailing replica of the HMS Beagle, the little ship that changed the world.

A fortnight ago we launched a caption contest for the provocative image below, originally taken from Time's negative review of Expelled. We received twenty-six highly humorous entries, but there was one that towered, marble head and shoulders, above the rest, both for its comic value and also for the amount of work involved in realising it.

And so, without further ado, I give you the (slightly fishy-smelling) hands down winner; it's an animation by the geniuses over at Eclectech called "Ben Stein meets Darwin". Click the image below to view the animation, then come on back and read the runners-up below.

CLICK IMAGE TO SEE ANIMATION

And now for the best text entries, as judged by an expert panel of me, in order of submission:

Thank you to all who entered. To see all twenty-five text caption entries, just read the comments of the original post. It was definitely a worthwhile endeavour, not least because it gave us all some slapstickfish comic relief on a Friday afternoon.

*an elaboration of the commonly used web shorthand "ROFL" (rolling on the floor laughing)

More updates:

In the same vein, though not a caption contest entry sensu stricto, is this.

Though most people associate [the Origin of Species] and Darwin’s ideas generally with his voyage to the Galápagos and his study of finches there, his work with plants was far more central to his thinking, said David Kohn, a Darwin expert and science historian who is a curator of the exhibition.

Even in the Galapágos he focused on plants, said Dr. Kohn, who is general editor of the Darwin Digital Library of Evolution at the American Museum of Natural History. “He did not even label the finches,” he said. “He was fascinated by plants,” particularly the way their variation and sexual reproduction challenged the idea that species were stable, a key idea in botany at the time.

As Dr. Kohn writes in the exhibition catalogue, “plants were the one group of organisms that he studied with most consistency and depth over the course of a long scientific career” of collecting, observing, experimenting and theorizing.

Yes, at long last, an exhibition in appreciation of Darwin the botanist.

As visitors walk through the Botanical Garden they will be able to follow an illustrated maps of the tree of life — the plant part of it, anyway — that tell them where the plants they can see fit in the evolutionary framework.

Oh, I am going to love this (did I mention I am going to New York next week?).

The tree of life exhibits, comprising an unusual mix of living plants, laboratory expertise and historical documents, show that many plants are surprisingly close relatives of others that seem quite different, a concept that helps botanists when they look for likely sources of useful plant chemicals or worry about maintaining biodiversity.

For example, “squashes and oaks are related,” said Dennis W. Stevenson, the garden’s vice president for laboratory science. “Who’d a thunk it?”

But while many branches move off simply and neatly in ways botanists understand — they are “totally resolved,” Dr. Stevenson said — other evolutionary branchings occur in clumps called polytomies, areas where the family history of plants is still unknown.

Read: this exhibition is clearly not afraid to put the realities of living science on display. Hurrah!

Garden officials recognize that there are those who challenge Darwin’s ideas, but for them there is nothing controversial about them. “Our whole science is based on evolution,” Gregory Long, the Botanical Garden’s president, said, as he surveyed the team of horticulturalists installing the flowers that replicate Darwin’s experiments.

“It’s the heart of our science,” he said. “We wouldn’t be here if it hadn’t been for Darwin.”

If you've ever wondered what happened to the HMS Beagle, this is your week!

On Monday we received a broad brush overview of the history of the ship from her birthplace at Woolwich dockyard in London, and we heard some rather moving reflections by Robert Prescott, Professor Keith Thompson and Gordon Chancellor on the irony of her anonymous end in light of her now-famous contributions to science. Listen again to Episode 1 and read my mini-review.

On Tuesday we were swept along to Cambridge with Robert Prescott to learn more about Darwin's own thoughts about the little ship that was his home for five years. Listen again to Episode 2.

Today it's back to London, to the National Archives at Kew, and then down to Paglesham in Essex where the Beagle quietly lived out her tenure as a Coast Guard watch vessel; treasures emerge from the mudflats, but the mystery is still not solved. Listen again to Episode 3.

22 April 2008

Just to say that now you can not only listen again to Episode 1(and read my mini-review), but also Episode 2, in which Robert Prescott visits Cambridge and reads excerpts of Darwin's letters home from the Beagle, and in which we learn that seasickness seems to make people a just a wee little bit grumpy.

As everyone knows, Earth Day is Everyday. But today, Earth Day is also--well--today. So why not celebrate by listening to the Earth Day 24-hour webcastathon, which starts exactly 1 hour from the time of this posting, that is, Midnight GMT (= 1:00 AM London, = 8:00pm Eastern Daylight Time).

The theme is "The Other 71%" in reference to the amount Earth's surface covered with ocean. You can even join a chat room while the webcasts are live-streaming, a splendid chance to harass Kevin and Rick ask intelligent questions about the marine environment!

21 April 2008

This week we are treated to a daily 15-minute dose of the history of the HMS Beagle on BBC Radio 4. Today, maritime historian Dr Robert Prescott begins his journey at Woolwich Dockyard in London, where he recounts his searches for the final resting place of the little ship that carried Charles Darwin around the world. Listen again to Episode 1.

Mini-review: The series starts off with a bang, giving us a star studded programme featuring not only Dr Prescott but also Professor Keith Thompson (Beagle biographer) and Dr Gordon Chancellor (archivist and Beagle historian). For me, the highlights were:

Professor Thompson's story of his quest to find the Beagle's original plans at the National Maritime Museum - which turned out to be just a set of coloured annotations to a generic plan for ten-gun brigs.

Robert Prescott saying, "for the ships officers and crew it must have been like a journey to the moon."

Gordon Chancellor telling us, in his own words and in the words of Charles Darwin, the riveting story of his father's painting Sorely Tried, right, in which the Beagle nearly meets her end off of Cape Horn on 13 January, 1833.

The majestic strains of choral music used to great effect at the end of the episode, as a kind of requiem to the Beagle and her glorious tenure, over which Robert Prescott says rather wistfully, "I like to imagine the Beagle during those later years, just sitting quietly in the river Roach as an old lady, reflecting on her glory days. By then she would have been tired, battered and faded, her timbers beginning to rot; but within those timbers were the memories of what she'd achieved, the extraordinary places she'd been, the storms she'd weathered and the men she'd carried."

19 April 2008

It's a cold, rainy spring Saturday in London; what better to do than spiff up the blog? Yes, I'll be sweeping out the dust e-bunnies by consolidating redundant labels, updating the blogroll, and adding a few new and exciting widgets and other things to the sidebar, all with fellow blogger Peter McGrath's approval of course. To top it all off, quite literally, We'll be putting up a spiffy new title banner. So, don't be surprised if you visit us today and happen to catch us amidspiff and things look a little funny. Rest assured it'll all be sorted out ASAP.

On this day in 1882, Charles Darwin passed away. New this month on Darwin Online is this obituary penned by none other than Thomas Henry Huxley. Read and be moved:

CHARLES DARWIN

VERY few, even among those who have taken the keenest interest in the progress of the revolution in natural knowledge set afoot by the publication of the "Origin of Species"; and who have watched, not without astonishment, the rapid and complete change which has been effected both inside and outside the boundaries of the scientific world in the attitude of men's minds towards the doctrines which are expounded in that great work, can have been prepared for the extraordinary manifestation of affectionate regard for the man, and of profound reverence for the philosopher, which followed the announcement, on Thursday last, of the death of Mr. Darwin.

Not only in these islands, where so many have felt the fascination of personal contact with an intellect which had no superior, and with a character which was even nobler than the intellect; but, in all parts of the civilised world, it would seem that those whose business it is to feel the pulse of nations and to know what interests the masses of mankind, were well aware that thousands of their readers would think the world the poorer for Darwin's death, and would dwell with eager interest upon every incident of his history. In France, in Germany, in Austro-Hungary, in Italy, in the United States, writers of all shades of opinion, for once unanimous, have paid a willing tribute to the worth, of our great countryman, ignored in life by the official representatives of the kingdom, but laid in death among his peers in Westminster Abbey by the will of the intelligence of the nation.

It is not for us to allude to the sacred sorrows of the bereaved home at Down; but it is no secret that, outside that domestic group, there are many to whom Mr. Darwin's death is a wholly irreparable loss. And this not merely because of his wonderfully genial, simple, and generous nature; his cheerful and animated conversation, and the infinite variety and accuracy of his information; but because the more one knew of him, the more he seemed the incorporated ideal of a man of science. Acute as were his reasoning powers, vast as was his knowledge, marvellous as was his tenacious industry, under physical difficulties which would have converted nine men out of ten into aimless invalids; it was not these qualities, great as they were, which impressed those who were admitted to his intimacy with involuntary veneration, but a certain intense and almost passionate honesty by which all his thoughts and actions were irradiated, as by a central fire.

It was this rarest and greatest of endowments which kept his vivid imagination and great speculative powers within due bounds; which compelled him to undertake the prodigious labours of original investigation and of reading, upon which his published works are based; which made him accept criticisms and suggestions from any body and every body, not only without impatience, but with expressions of gratitude sometimes almost comically in excess of their value; which led him to allow neither himself nor others to be deceived by phrases, and to spare neither time nor pains in order to obtain clear and distinct ideas upon every topic with which he occupied himself.

One could not converse with Darwin without being reminded of Socrates. There was the same desire to find some one wiser than himself; the same belief in the sovereignty of reason; the same ready humour; the same sympathetic interest in all the ways and works of men. But instead of turning away from the problems of nature as hopelessly insoluble, our modern philosopher devoted his whole life to attacking them in the spirit of Heraclitus and of Democritus, with results which are as the substance of which their speculations were anticipatory shadows.

The due appreciation or even enumeration of these results is neither practicable nor desirable at this moment. There is a time for all things—a time for glorying in our ever-extending conquests over the realm of nature, and a time for mourning over the heroes who have led us to victory.None have fought better, and none have been more fortunate than Charles Darwin. He found a great truth, trodden under foot, reviled by bigots, and ridiculed by all the world; he lived long enough to see it, chiefly by his own efforts, irrefragably established in science, inseparably incorporated with the common thoughts of men, and only hated and feared by those who would revile, but dare not. What shall a man desire more than this? Once more the image of Socrates rises unbidden, and the noble peroration of the "Apology" rings in our ears as if it were Charles Darwin's farewell :—

"The hour of departure has arrived, and we go our ways—I to die and you to live. Which is the better, God only knows."

16 April 2008

Cue trumpets: Matt Brown has just announced that the Royal Institution in London will host a European science blogging conference later this year, exact date yet to be determined. More info here including a chance to weigh in on date selection. Two science blogging conferences in one year (the other one being the SBC in January): I have officially died and gone to heaven.

Hope to see you there (in London ...and heaven ...even though I don't believe in that ...not that there's anything wrong with believing in that ...if you go in for that sort of thing).

13 April 2008

This is the first in a series of guest posts in Spanish by Argentinian biologists and writers Hilda Suárez and Alejandro Balbiano, early and enthusiastic supporters of The HMS Beagle Project. We feel it is wholly fitting that there should be a voice for the Beagle Project en español, and we hope this series helps to expand awareness of the project in South America, the central venue of the Voyage of the Beagle. ~ nunatak

Now there's a 12-part documentary TV series about it called Garbage Islandon the online broadcast network VBS.tv. Parts 1-5 are already available to watch online. To get you started, here's Part 1:

Warning: adult language

VBS correspondent Thomas Morton wrote about his experience on the Alguita...

Before this trip, I was never all that crazy about the ocean. I’ve always appreciated the fact that it generates the majority of the world’s oxygen and keeps us nice and far from places like Britain, but in terms of any sort of awe or “respect” it just never happened. I would say I looked at it less as the primeval womb of all terrestrial life than as an excessive amount of water you sometimes have to fly over...

...Needless to say this whole journey ended up overturning my expectations about the Garbage Patch, as well as just about every misconception I’ve ever held about the sea, environmentalism, consumption, barfing, knots, pollution, humanity, and myself...

10 April 2008

Yesterday afternoon Bora and a small group of London area bloggers and readers came over to the Natural History Museum for a bit of a look-see 'round the place. Our first point of call was rather sombre but nevertheless a must: Professor Steve Steve paid tribute to his famous cousin, Chi Chi the giant panda.

The horror.

Initially disturbed by the sight of his kin so crudely stuffed and put on display for all to see whilst enjoying cups of tea and "coprolyte cupcakes" in the museum cafe, Steve Steve's sadness turned to admiration when he noticed that even after having been killed, stuffed and locked in a diorama for several decades, Chi Chi still seemed to manage a regular diet of bamboo.

Next I took our bloggers to see the Zoology department's impressive spirit collection (no, not a collection of spirits, but a collection in spirit). The highlight, as always, was the "tank room" where the really big specimens lurk. Most of them are in big ground-glass jars, but specimens too big for the biggest jars are put in metal containers the lids of which have to be removed with a system of chains and pulleys.

The biggest of all is Archie, the giant squid, named after its genus Architeuthis. As you can see, Archie has her (yes, Archie is a her) own special container, which is especially conducive to drop-jawed ogling.

At the other end of the room in a dim little cabinet are some small but very special specimens: fish collected by Darwin during his time aboard the Beagle. In all the excitement, I seem to have forgotten to take photos of them, but I'm hoping some of the others will post theirs in the near future (update: Mo answers the call). After the tank room, we stopped off for a quick group shot in the Darwin Centre.

Having worked up a thirst in the tank room (mm mm mm, industrial methylated spirits...), we went across the street to the Queen's Arms (more pictures expected from the other bloggers) and then on to Daquise for an excellent Polish meal followed by rounds of vodka.

"English Heritage's offering for the bicentenary of Darwin's birth next year is to be developed around its Down House exhibition, with the help of Designmap.(snip) As well as commemorating Darwin's bicentenary and the 150th anniversary of the publication of On The Origin of Species, English Heritage aims to clarify Darwin's theories to the public through a revamped permanent exhibition space at Down House in Kent, where Darwin lived. (Excellent - ed. Snip.)

English Heritage interpretation officer Jenny Cousins explains that funding released by the sale of neighbouring property Buckston Browne to the Charles Darwin Trust in 2004 has enabled the £1m development.

If you have blood pressure pills, prepare to neck a few now.

'One of the things that came out of the visitor research was that the public knows who Darwin is, but doesn't really know what he did, what his theories are, or why he's important. It's Designmap's job to tell the story,' says Cousins."

Congrats to Designmap, and their advisory committee certainly know their Darwin onions, but it does make one wonder just what the dickens has been going on in biology and history classes the length and breadth of Britain all these years that the bulk of people asked don't know 'really know what he did, what his theories are, or why he's important.'

9 April 2008

A lot, a lot of people have contacted us asking to sail with us: some want to do science, some just have the kind of enthusiasm to come and be part of something iconic and great. Those of us who've sailed for any length of time know it's not all taut sails against blue skies and sun-warmed decks. As Charles Darwin found out:

7th April 1833Our usual luck followed us in the shape of a gale of wind; being in the right direction we scudded before it; by this means we run a long distance, but it was miserable work; every place dark wet & the very picture of discomfort.

Yes Charles been there, thinking I could be this miserable staying at home and slamming my hand in a car door every fifteen minutes. At least I'd be warm and dry between the discomfort. Then the sun comes out, the sea calms, the sailing becomes sweet and the wet and discomfort is forgotten.

Sometime after Darwin's lugubrious 7th April entry things perk up and Captain Fitzroy packs the sail on:9th April 1833The weather to day is beautiful; it is the first time for three months that studding sails have been set. We attribute all this sun-shine & blue sky to the change in latitude; small although it be. We are at present 380 miles from the Rio Negro.

And there is no finer thing to be doing, no finer place to be than at sea. (The studding-sails are the ones stuck out to left and right on this pic of Beagle - they were rigged in light airs. In tar-talk, she would be described as 'flying stuns'l aloft and alow'. It's like putting the spinnaker up on a modern yacht, the weather's right, the sailing's good - all is right with the world.) Just making the point that you want to come on the Beagle, sometimes it'll be wet, cold, bouncy and cramped. But Darwin put up with that and seasickness for five years. Dude.

The Malacological Society of London announces a one day symposium ‘Speciation in Molluscs’ to coincide with the Annual General Meeting of the Society. Talks will be given by invited speakers at the forefront of this field. This meeting will be of interest to evolutionary biologists, biogeographers, students, post-doctoral researchers and researchers.

Places are limited, and registration is required. Registration is FREE and includes a wine reception to follow the meeting. Please let us know if you wish to bring a poster, and provide an abstract. Send applications by e-mail to Suzanne Williams: S.Williams (at) nhm (dot) ac (dot) uk.

8 April 2008

BBC Radio 4 are running a 5-part series on HMS Beagle 21-25 April, 3.45-4pm BST. The Beagle Projecteers will bookend the series, appearing on 21st and 25th. Report of the day's freezing recording in Woolwich at the slip where HMS Beagle (1) was built in 1820 here.

is on at the Royal Ontario Museum, and Beagleblog roving reporter Glendon Mellow kindly went to review the exhibition for us. Now by way of thanks go visit his gallery and blog. Glendon writes:

Posters of a man in black and white, a green iguana, and bright pink orchids abound in transit shelters across Toronto. Darwin: The Evolution Revolution exhibit is on at the R.O.M., my hometown's museum that has caused so much buzz in the past year after being "crystallized". To introduce myself, my name is Glendon Mellow, and I am honoured and thrilled to be writing this review for The Beagle Project Blog. I am an artist in awe of science who lives in Toronto, Ontario, Canada, and I blog at The Flying Trilobite. I was approached by Humble Woodcutter of The Free Range Academy to write this review for The Beagle Project Blog. Pictures were not allowed in the exhibit, so I have done my best to provide.

The ExhibitBy following a chronological look at Darwin's life and achievements, the exhibit seduces and beguiles using only facts. He was an ordinary man, albeit with the foibles, interests and intelligence that made it possible for him to think deeply on the natural world, and much time is spent on this at the beginning. The exhibit pulls no punches with evolution by natural selection later in. In that matter-of-fact, writ-large-with-no-punctuation way that museums do so well, evolution as a proven fact is stated again and again. As it should be.

As a visual kind of guy, let me give you the rough sketch of what the exhibit feels like. The exhibit is below ground, under an overhang in the R.O.M.'s Staircase of Wonders; the overhang is perfectly suited, as it displays "Mammal Weaponry" with everything from antlers to a narwhal tusk. The main portion of the exhibit features darkly stained wooden glass cabinets. Small curios featuring antique magnifying glasses of interesting construction dot the exhibit, each enlarging some beetle or hummingbird or plant or fossil. The piece that most struck me with a shiver of Darwin's presence included a small drawing of Leptura quadrifasciata in a letter to his cousin, inscribed, "the insect is more beautiful than this drawing". (I could go on and on about an 1840 lithograph by George Scharf of a Toxodon platensis skull fossil, but I really shouldn't.)To me, the importance of information in a museum is paramount, and this exhibit delivers. You can catch brief titles, or spend a couple of hours looking over everything. As I have often observed at the Toronto Zoo, it is amazing how some people have opinions on displays without first reading them. At the diorama of the Galapagos seashore, which features robustly stuffed marine iguanas and a couple of green iguanas, I over heard one young man ask his girlfriend, "Those real?" to which she replied, "Yeah, but they're like dinosaur-age iguanas". They then moved forward to read the placards. There are so many things I did not know: I had no idea he discovered Megatherium; was related to the Wedgewoods; or argued his Captain about the immorality of slavery and was almost left on shore because of it. I hope the curators are quite proud of how this exhibit came together; it is a treasure. Live frogs, an iguana, tortoises, orchids, venus fly-traps, fossils of Pleistocene megafauna, skeletons of bats, primates and the homology of forelimbs feed the eyes and entice the curious.

Reactions"I wish this guy was still alive; I'd introduce him to God."One stomping teenage girls' commentary notwithstanding, the people I observed seemed to be curious and enjoying themselves. There are five short movies playing and three were well-attended, the last two being grouped so close together their sound overlapped. After hearing palaeontologist and trilobite-rockstar Richard Fortey say something to the effect of biodiversity being "…all the spiritual present in the world I need," I overheard one patron utter, "Works for me." A nearby wall about current controversies remained well-attended. The video featuring Fortey was on a vertical flatscreen on a pillar near the large evolution by natural selection exhibit. It was set at an average person's height, with the commenters' addressing the viewers on their own level. It featured Francisco Ayala, Eugenie Scott, Niles Eldridge, Georgia Dunston and Kenneth Miller. The natural selection exhibit is clear and easy to follow. Evolution has been observed in the lab amongst bacteria, which reproduce quickly. The connection of slower, larger reproducers from eohippus to the modern horse is clearly made.

A child's perspectiveOn this visit, my wife and I brought our six-year old nephew, who for the sake of his anonymity I shall refer to as Obi-Wan. An easily overlooked workbook is at the entrance, (in both official languages, mais oui) urging children to become Darwin's assistant. The booklet was terrific, starting Obi out by investigating the two tortoises and comparing their features. Many times our nephew Obi crouched down on the floor after figuring out what the answer was that he needed to finish another section. We received a lot of curious looks and some comments from passers-by. When Obi was filling out some true or false answers and he guessed at one, my wife pointed out that he shouldn't guess, as he did not yet have any evidence. He was incredibly excited when he found the answer, and I feel that lesson may stick. At another point, Obi was moved to draw abruptly, and asked to borrow my sketchbook so he could draw the dwarf armadillo on display next to the glyptodont. He spent about five minutes leaning against the angled placard, and drew this brilliant armadillo, starting with its detailed toes.A video screen found in a few areas deftly illustrated natural selection better than my bungled attempt. It features bright orange and green bugs zipping around a background of green leaves. As the bird (clicking a button), Obi clicked the obvious orange bugs out of existence –almost! Then the screen turned the shade of orange as the orange bugs! The green ones are being eaten! The kids' area at the end was almost an afterthought, even with their version of The Beagle.

ConclusionThe exhibit is well-displayed and rigorous in its main points; Darwin was a normal, decent person; evolution by natural selection is true and makes sense; and though controversy remains, the natural world is deserving of the wonder Charles Darwin gave it. I highly recommend it, and hope it is indicative of the pursuit of displaying scientific truths about the natural world that we should expect from institutions such as the Royal Ontario Museum.

When I asked my nephew what he thought the skeleton of the chimpanzee hanging from the tree was, he studied it and asked, "a person?"

"Yeah, close!" I replied.

Many thanks Glendon, Mrs Mellow and Obi-Wan especially for the Flying Trilobite and Obi-Wan original art. A cup of tea and slice of cake awaits aboard when we get Beagle across the Atlantic. Bring your paints. Now someone go and commission a socking great painting from Glendon.

7 April 2008

If you are anywhere even remotely close to New York City, get ye to the new exhibition at the New York Botanical Garden, Darwin's Garden: An Evolutionary Adventure. It is curated by none other than David Kohn, one of the world's foremost Darwin scholars. The exhibition includes a recreation of Darwin's garden at Down House in England and his wonderful "weed garden" experiment, but...

The cornerstone of the Garden-wide show is an exhibition of Charles Darwin's original manuscripts, field notebooks, plant collections, and other historical documents chronicling Darwin's progression from a boy with an interest in plants to an evolutionary botanist who revolutionized the world's view of life.

The exhibition's more than 60 rare books and objects, starting with a portrait of him as a young boy holding a plant, tell the story of Darwin's life-long relationship with plants. A facsimile of a herbarium specimen he collected as a student represents, in part, his early influences and his studies at Cambridge University. Sketches of flowers and journal entries such as his exuberant reaction upon first encountering a tropical forest bring to life his five-year voyage on the HMS Beagle to the Galápagos and other lands,as his theories of natural selection and evolution began taking shape.

Darwin's rough drawing of a tree of life under the words "I think" shows his visualization of the interconnection of species, which led to the writing of his seminal work, On the Origin of Species. His Experiment Book contains several of his botanical experiments, color photographs, and engravings. It highlights Darwin's exhaustive plant observations and investigations in his later years on plant sexuality (the role of flowers, including pollination and co-evolution of plants and their pollinators) and sensitivity (how plants respond to touch, light, gravity, and chemical substances).

6 April 2008

Peter and I are going to be interviewed by Mike Haubrich a.k.a. Tangled Up in Blue Guy on "Atheists Talk", the talk show of the Minnesota Atheists on AM950 KTNF today, Sunday, April 6 at 9am Central Daylight = 3pm London (GMT+1). Mike says if you are out of reach of the signal you can still stream online as long as you enter a Minnesota zip code (55112 works).

Mike Haubrich in the studio, preparing toearn his spot in the new Beagle's crow's nest "tops".

5 April 2008

It's been over a month--that's about seven thousand blog years--since my PLoS ONE paper came out and I'm only just now getting around to giving it a proper blog treatment. In defense of my tardiness, the paper is pretty small-fry in terms of its newsworthiness. It didn't even get a press release (though maybe that's a good thing). In other words, it's still fresh to the blogosphere. Well, that's my excuse at least.

At first I wondered: is this normal? Blogging on one's own peer-reviewed research, that is? But Bora Zivkovic (PLoS ONE Online Community Manager/crazy uncle of the science blogging community) and Liz Allen (PLoS Director of Marketing and Business Development) have made it clear that giving my own paper the BPR3 treatment is not only normal, it is expected.

There are several ways I might approach writing this post. The most obvious is to simply summarise the paper In Plain English. Problem is, I've already done that by writing a news blurb for the Natural History Museum website, and I don't really feel like repeating myself (though of course I will, but only to the extent to which it is necessary to tell my story).

A second approach is to critically analyse the paper. But you can see the problem with that right away: since I wrote it, I've already critically analysed it. Critical analysis necessarily belongs to someone who isn't an author on the paper.

A third approach, and the one I am going to go with, is to tell the whole story of this project: the blood, sweat and occasional tears, not just the part that appears in the paper itself. This will be by far more interesting than a simple recap of the key findings of the paper itself (which, as I said, you can get elsewhere). Moreover, the whole story illuminates the reality of the scientific process in a way that's intelligible to the non-scientist; well, that's my aim anyways.

This is not my study organism.

About four years ago I was working as a postdoctoral research assistant to Professor Richard Bateman (then Keeper of Botany at the Natural History Museum and president of the Systematics Association) on two very closely related species of British terrestrial orchid, neither of which is pictured at right. I could tell you which species we're really working on but then I might have to shoot you. Okay, it's not that serious--Richard's spoken publicly about this story--but this work hasn't been published yet and I wouldn't want to steal our peer-reviewed thunder on a blog.

So, back to our pair of mystery orchids. Though they are so closely related that their designation as separate species is debatable, the two can nevertheless be easily distinguished by their floral morphology (the size and shape of the various parts of the flower). At the time we began, there was some anecdotal evidence that the two might be discriminated by DNA as well, and thus it was our intention to follow this up with a more focused DNA sequencing project to see if the difference in floral morphology correlates with unique genetic signatures.

Using that knowledge as a foundation and context, we could then perhaps set up an experimental system to pursue the specific genetic underpinnings of the different morphologies. And that's really the exciting part: ferreting out the developmental-genetic mechanisms of evolutionary change (an undertaking called "evo-devo", about which readers of a certain atheist proselytiser's blog will already be aware).

To query the genomes of our two species, I used a common but no less wonderfully clever lab technique called Polymerase Chain Reaction (PCR), coupled with the equally clever Sanger sequencing (which we do using fancy dyes and capillary tubes these days), to obtain short (less than 2000bp) sequence reads from a handful of gene regions that had been previously shown to be useful in reconstructing evolutionary relationships within and among species.

After sequencing more than 10,000bp-worth of these regions from each of four specimens (two from each species), I could not find a single difference between the species. Well, there was one difference, but it didn't sort by species. This kind of evidence doesn't necessarily prove that these aren't different species (while DNA can in some cases identify species it cannot--or at least should not--be used to define them except as a last resort), but it does suggest that the morphological difference that defines these species has evolved relatively recently, that is, so recently that the gene regions I tested have not had a chance to evolve since then. This brings the evo-devo question tantalisingly close: we may in fact have caught this species in the act of splitting in two, in other words, we may be witnessing the origin of species.

But if we couldn't find any genetic variation to distinguish the two species, how were we going to proceed with making our wildest evo-devo dreams come true? There are other methods for detecting genetic variation within and among species (AFLP, microsatellites, etc. for those who care), but I'm not going to go into details on those except to say that they involve a laborious preliminary optimisation phase every time they are going to be applied to a new group of organisms. So I started sniffing around for a different technique, a technique that perhaps could bring the high-throughput technologies of the genome revolution to bear on biodiversity.

That was when I saw a conference abstract presenting a new technique called Diversity Arrays Technology, or DArT. DArT builds on an existing technique called a DNA microarray that is used to detect small genetic differences among people and other organisms for which the full genome sequence is known. The innovation of DArT is that it uses microarrays in a new way so that no prior knowledge of the genome is required. It immediately occurred to me that this opened the possibility that all of biodiversity, not just a handful of so-called 'model organisms', could be examined using the tools of the genome revolution.

DArT was originally used to map naturally occurring (not genetically engineered) traits in economically important crop plants like rice and barley, but hadn't yet been tested on 'wild' plants (or animals). I asked Richard if he thought it was worth pursuing DArT to tackle our orchid speciation question and this was met with great enthusiasm and I was encouraged to write a grant proposal for a small pot of internal funding. I had a couple of project-planning phone calls with Andrzej Killian, inventor of DArT and director of Diversity Arrays Technology Pty Ltd, based in Canberra Australia, and it looked like we were set to give it a shot. Ah, those were the heady days...

But here our story takes a strange twist--the sort of twist that doesn't make it into the peer-reviewed literature. See, unfortunately at this point, there was a shake-up in departmental leadership and the politics of power found their way into the very heart of myelittle project. Due to past and present departmental sensitivities I will not discuss it here except to say that it resulted in a change in both the plants and the biological questions to which DArT would be applied in my proposal. Fortunately, despite this last minute change in line-up, the proposal scored very high marks from the committee and was funded in full.

And so I began the process of testing whether DArT could work successfully within and among wild plant species, as opposed to domesticated, inbred strains of agricultural crops in which DArT had already been proven to work. I applied DArT to two different groups of plants. The green spleenwort Asplenium viride and the moss Garovaglia elegans (left) were chosen for the trial to reflect existing Botany department areas of expertise. Professor Harald Schneider, Dr Johannes Vogel and Dr Stephen Ansell are actively researching the evolution of Asplenium and Dr Angela Newton and Dr Niklas Pedersen the evolution of Garovaglia. They assembled an appropriate selection of specimens and posed specific evolutionary questions that might be addressed by the DArT technique.

I wouldn't be writing this if it hadn't worked. DArT gave us a collection of 1349 new genetically variable regions to work with in order to examine the relationships within and among Asplenium and Garovaglia species. My co-authors' analysis of the DArT data corroborated known relationships and also revealed some new patterns. But the key result was that DArT could be successfully used on non-model, non-domesticated, non-inbred, that is, wild plants.

DArT also proved adept at detecting hybridisation, which is very common in plants, and even mixed-specimen samples. And when I obtained the DNA sequence reads of a smattering of the DArT regions we recovered, I found that quite a few matched known genes in that great big DNA database in the sky, GenBank, and one even matched one of the proposed plant DNA barcoding genes, trnH-psbA (more on DNA barcoding in a previous post).

My hope is that this study will give others the confidence to apply DArT to their research groups, and that this will speed the rate at which patterns and processes in evolution can be understood, and genetic diversity conserved in the wild.

And in case you were wondering whether I still have hopes of applying DArT to our "orchid problem", all I can say now is: watch this space!

Excitement! My friend and colleague at the Natural History Museum, Adrian Glover, is blogging from Antarctica about his deep sea research there. Yes, you read that right, folks, blogging from Antarctica.

*seethes with envy*

More specifically, Adrian is blogging from the RRS James Clark Ross, where he says "dinner is shirt and tie, with cocktails in the bar before dinner, wine on the tables and fine silver to eat with". Ahhh, the British.Adrian's blog, News from the world of deep-sea whale-falls, polychaete worms and Antarctica contains such gems as the photo at right which I think should be titled "Antarctic deep sea still life with whale-fall and crab".

Adrian's blog conveys the excitement of deep sea scietnific discovery with a dash of maritime history and real-life accounts from life aboard an Antarctic icebreaker. Here are some teasers:

On the James Clark Ross, we press a button to stop the ship, and another button to lower a trawl 5000m over the side. On an 18th century sailship, just stopping the ship and holding position would be a feat, let alone finding the power to deploy thousands of metres of wire. Pre-19th century mariners did not really care about the deep sea. It was enough to know there were no rocks to run into and enough water to bury the dead.

- - -

With me on the James Clark Ross, I have three experimental moorings designed by OceanLab in Aberdeen, each consisting of a whale bone or wood package, and a special acoustic transponder which acts like an underwater marker beacon to any submersible or remotely operated vehicle (ROV).

- - -

My interest in polychaete worms has kept me busy on this cruise, not just in preparing the moorings, but in working up the thousands of specimens we have brought up from Pine Island Bay and the Amundsen Sea. These include the largest predatory polychaete I have ever seen – with jaws large enough to take off a small finger. But that is another story!

I'd say get over there and leave comments but Adrian's blog doesn't allow comments. Phooey. I'll see what I can do. It'll help if I have some positive comments from the blogosphere to pass along to him. Please use this post a place to comment on Adrian's blog and then I can show him what he's missing!

2 April 2008

At right is their take on creationism/ID (click for a larger view). Unfortunately, it's more factual/historical than critical, and it strikes me as not taking a strong position. The strongest bit is the last sentence ("[Judge John Jones'] judgment made it clear that ID could not be considered a valid scientific theory") but even here Wellcome is simply giving Judge Jones the last word instead of taking a position against ID, as I believe any institute with Wellcome's authority should.

Unfortunately, the rest of the booklet contains more of the same. There's certainly lots of information about evolution that is presented in an accessible if rather cartoonish way. They do a particularly good job explaining the fact that all species are descended from a common ancestor and they go into quite a lot of good detail about genes and evolution.

But then they also give a lot of space--a full quarter of the 16 page booklet--to religious voices who, though none deny evolution outright, make anti-scientific statements like "God is a given, there is no doubt He exists" and then go on explain how this is rationalised to fit with scientific thought (i.e. God created the world using evolution). This viewpoint, that religion can and should be fitted around--or melded with--current scientific knowledge, is often called "God of the gaps" and it can be just as damaging to religion as it is to science.

Worse, they call this section of the booklet "Real Voices", which provides just the opt-out that a reader who might want to deny or rationalise evolution is probably looking for. In other words, Wellcome never comes out and says that while these voices may be real that they are not necessarily right.

In the end, by giving religion a lot of space in an educational booklet about evolution, Wellcome is, by default, legitimising the presence of religion in the science classroom.

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